Matteo Aldeghi
Matteo Aldeghi
**Use-cases/examples of this new feature** Model training on data from DNA-encoded library screening. **Desired solution/workflow** Implement the custom loss described in this paper: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.2c00041 **Discussion** It could be implemented as...
`Cma` and `Phoenics` (possibly others) create folders/files when they run (called `outcmaes` and `SearchProgress`, respectively). We could cleanup these folders/file after we terminate the planners.
From #2 : the following packages are required to compile the documentation: - `scikit-learn` - `sqlalchemy` - `matplotlib` - `seaborn` - `m2r`
I get this message many times if I instantiate a `Dataset` object without assigning it to a variable (in Jupiter notebook), e.g.: ``` Dataset(kind='colors_bob') >>> ATTR _ipython_canary_method_should_not_exist_ >>> ATTR _ipython_canary_method_should_not_exist_...
The `alkox` parameter space, defined in its `config.json`, does not match the data in the csv file. The temperature is expected to be between 60 and 140: ``` dataset =...
When trying to generate the docs for the `databases` subpackage, `sphinx` returns an error about a maximum recursion depth: ``` RuntimeError: maximum recursion depth exceeded while calling a Python object...
- [ ] SMAC (https://github.com/automl/SMAC3) - [ ] ENTMOOT (https://github.com/cog-imperial/entmoot)
This adds the option to use detectEquilibration from the timeseries module to detect the equilibrated region of the windows automatically. It modifies the uncorrelate function to do this. When using...
As possible enhancement, I wonder whether it might be useful to have an option to determine the windows' equilibration period automatically as suggested by John Chodera here: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00784 It could...
A possible small enhancement: since for absolute calculations there is a also a restraints component other than coulomb and vdw, it could be good to have the free energy of...